2013 Fiscal Year Annual Research Report
プラナリアゲノムプロジエクト：ゲノム情報を用いた再生遺伝子ネットワーク解析
| Project/Area Number |
13J01078
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| Research Institution | Kyoto University |
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Principal Investigator |
安 洋 京都大学, 理学研究科, 特別研究員(DC2)
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| Keywords | planarian / enome / nou-darake / enhancer |
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| Research Abstract |
Partl : Draft genome of Dugesia japonica planarian
Dugesia japonica is a free living freshwater flatworrn. It is asuperb model for studying regeneration, nervous system evolution and development. To deeply understand this model animal and discovery the generegulatory network of brain formation, its genome information is necessary. However, Dugesia japonica has ahighly heteroZygous genome containing a very high number of repetitive sequences, which notoriously make the de novo genome assembly extremely hard work based on next-generation sequencing nowadays. To accomplish this hard task, we recently combined de novo and reference-guided assembly, and then assembled a1.03 Gb draft genome. Although the nature of the sequence of Dugesia japonica genome interfered with the continuity of the assembled contigs, this draft genome can still cover 99.3% of EST sequences, and distinguish all coding genes' exon-intron structures. In addition, conserved non-coding sequences were fbund by comparing with Schmidtea mediterranes's genome, which are good candidates for regulatory elements.
Part IINDK enhancer activity analysis
Previous evidence on planarian shown nou-darake (NDK) involved in restricting brain formation to theanterior region of the body. The similar expression pattem between NDK in planarian and Fgfrll (the homologue of NDK in vertebrate) in xenopusemblyo indicated that NDK has conserved function during evolution. To prove this hypothesis, at first, we found a 150bp conserved noncoding sequence between human, mouse and xenopus by genome comparison, and then confirmed the enhancer activity by transgenic xenopus embryo. Furthermore, from the new assembled Dugesia japonica draft genome in the Part I result, we found one conserved sequence has an identical transcription factor binding site of the just proved vertebrate NDK enhancer.
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| Current Status of Research Progress |
Current Status of Research Progress
1: Research has progressed more than it was originally planned.
Reason
High heterozygous genome and repetitive sequences in genome are two notorious interference factors interfering de novo genome assembly. Unfortunately, in the case of Dugesia japonica planarian, weencountered both of the two bad factors. However, by combining de novo and reference-guided assembly, Isucceeded in assembling the draft genome of this species.
At the same time, I successfully discovered and proved a vertebrate conserved NDK enhancer, whichindicates a conserved NDK involved brain formation mechanism in vertebrate. Furthermore, from the plallarian genome I assembled, I also fbund a similar enhancer in planarian. It is a big progress in our research, which may indicate an animal evolutional conserved mechanism.
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| Strategy for Future Research Activity |
In the future, I will at frist refine the genome information, and perform genome annotation.
In addition, because I found a large number of planarian conserved non-coding sequences (good candidates of regulatory elements) ; I will pick out conserved sequences around some genes involved in braindevelopment, especially the NDK gene.
Furthermore, by analyzing the genome information and gene enhancer analysis, I plan to find out the NDKinvolved regulatory gene pathway during brain development and regeneration.
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Research Products
(1 results)
